Typical ion sources in mass spectrometry systems are operated at a constant temperature for ease of tuning, use and issues of stability. There are many forms of sample introduction for mass spectrometric ion sources such as those involved in liquid chromatography (LC) and mechanisms of ionization (electrospray, atmospheric pressure chemical ionization, etc.) or those for samples that are more suitable to being thermal volatized due to their stability such as gas chromatography or insertion probe (for those less stable). Although these source considerations apply widely they are easiest to illustrate by the technique of gas chromatography (GC). In GC, samples are separated by their volatility and partitioning between a mobile gas (carrier) phase and a stationary phase coated on some support such as the wall of a capillary column. As the temperature of the column and carrier gas changes (usually in a heated temperature bath or oven) the distribution of the sample components between the two phases changes and a separation is possible. As the temperature changes and the components partition into the carrier and through a variety of interfaces, enter into the MS ion source where they are ionized and eventually detected. Alternatively, components can be introduced to the ion source by probe, which performs a very crude separation solely by the heating of the probe tip on which the sample resides. Higher volatility components evaporate before the less volatile. In both these scenarios, temperature is used to “move” compounds into the ion source. In LC, a change in the mobile phase composition is used to elute compounds into the ionization region. But upon entering the ion source, many compounds show different tolerances to the temperature of their new surroundings. The pattern of the ion fragmentation and the total response (signal) are dramatically influenced by the ion source temperature. Compounds that are thermally sensitive will rapidly degrade in very hot ion sources and will show a decreased response. Compounds that elute (from the GC or probe) at very high temperatures will show very poor chromatography (broad peaks non-gaussian in shape) and low response in ion sources that are too cool. As a concession to robustness in operation, ion source temperatures have usually been kept very high to prevent condensation of analytes and matrices that may compromise source cleanliness. This situation often occurs in all kinds of sources and modes of operation including and not limited to electron impact ionization, chemical ionization (positive and negative mode), electron capture negative ionization mode (ECNI), photo-ionization etc. This effect is particularly pronounced in ECNI mode.
Recognizing that analytes have differing “optimum” ion source temperatures in terms of response, spectra, etc., and that other analytical concerns exist, such as robust operation, etc., to allow for continual optimization of ion source temperature by enabling changing ion source temperatures during the analysis continues to be an ongoing problem. These and other problems have been obviated and addressed by the present invention.